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<FONT color="green">001</FONT>    package edu.hawaii.myisern.model;<a name="line.1"></a>
<FONT color="green">002</FONT>    <a name="line.2"></a>
<FONT color="green">003</FONT>    import static java.util.Collections.emptyMap;<a name="line.3"></a>
<FONT color="green">004</FONT>    import java.io.File;<a name="line.4"></a>
<FONT color="green">005</FONT>    import java.io.FileNotFoundException;<a name="line.5"></a>
<FONT color="green">006</FONT>    import java.io.FileOutputStream;<a name="line.6"></a>
<FONT color="green">007</FONT>    import java.io.IOException;<a name="line.7"></a>
<FONT color="green">008</FONT>    import java.math.BigInteger;<a name="line.8"></a>
<FONT color="green">009</FONT>    import java.util.ArrayList;<a name="line.9"></a>
<FONT color="green">010</FONT>    import java.util.HashMap;<a name="line.10"></a>
<FONT color="green">011</FONT>    import java.util.HashSet;<a name="line.11"></a>
<FONT color="green">012</FONT>    import java.util.List;<a name="line.12"></a>
<FONT color="green">013</FONT>    import java.util.Map;<a name="line.13"></a>
<FONT color="green">014</FONT>    import java.util.Set;<a name="line.14"></a>
<FONT color="green">015</FONT>    import java.util.SortedSet;<a name="line.15"></a>
<FONT color="green">016</FONT>    import java.util.TreeSet;<a name="line.16"></a>
<FONT color="green">017</FONT>    import javax.xml.bind.JAXBContext;<a name="line.17"></a>
<FONT color="green">018</FONT>    import javax.xml.bind.JAXBException;<a name="line.18"></a>
<FONT color="green">019</FONT>    import javax.xml.bind.Marshaller;<a name="line.19"></a>
<FONT color="green">020</FONT>    import edu.hawaii.myisern.collaborations.jaxb.Collaboration;<a name="line.20"></a>
<FONT color="green">021</FONT>    import edu.hawaii.myisern.collaborations.jaxb.Collaborations;<a name="line.21"></a>
<FONT color="green">022</FONT>    import edu.hawaii.myisern.organizations.jaxb.AffiliatedResearchers;<a name="line.22"></a>
<FONT color="green">023</FONT>    import edu.hawaii.myisern.organizations.jaxb.Organization;<a name="line.23"></a>
<FONT color="green">024</FONT>    import edu.hawaii.myisern.organizations.jaxb.Organizations;<a name="line.24"></a>
<FONT color="green">025</FONT>    import edu.hawaii.myisern.researchers.jaxb.Researcher;<a name="line.25"></a>
<FONT color="green">026</FONT>    import edu.hawaii.myisern.researchers.jaxb.Researchers;<a name="line.26"></a>
<FONT color="green">027</FONT>    <a name="line.27"></a>
<FONT color="green">028</FONT>    /**<a name="line.28"></a>
<FONT color="green">029</FONT>     * Data Model for the MyIsern program.<a name="line.29"></a>
<FONT color="green">030</FONT>     * <a name="line.30"></a>
<FONT color="green">031</FONT>     * Provides access to researchers, organizations, and collaborations. Also includes methods for<a name="line.31"></a>
<FONT color="green">032</FONT>     * loading data from files and checking for dangling references between entities.<a name="line.32"></a>
<FONT color="green">033</FONT>     * <a name="line.33"></a>
<FONT color="green">034</FONT>     * @author Brian Jaress<a name="line.34"></a>
<FONT color="green">035</FONT>     * @auther Kevin English<a name="line.35"></a>
<FONT color="green">036</FONT>     * <a name="line.36"></a>
<FONT color="green">037</FONT>     */<a name="line.37"></a>
<FONT color="green">038</FONT>    public class IsernModel {<a name="line.38"></a>
<FONT color="green">039</FONT>    <a name="line.39"></a>
<FONT color="green">040</FONT>      // containers for the data<a name="line.40"></a>
<FONT color="green">041</FONT>      private Set&lt;Id&gt; ids;<a name="line.41"></a>
<FONT color="green">042</FONT>      private Map&lt;Id, Researcher&gt; researchers;<a name="line.42"></a>
<FONT color="green">043</FONT>      private Map&lt;Id, Organization&gt; organizations;<a name="line.43"></a>
<FONT color="green">044</FONT>      private Map&lt;Id, Collaboration&gt; collaborations;<a name="line.44"></a>
<FONT color="green">045</FONT>    <a name="line.45"></a>
<FONT color="green">046</FONT>      // files to load and save from<a name="line.46"></a>
<FONT color="green">047</FONT>      private String researchersFile;<a name="line.47"></a>
<FONT color="green">048</FONT>      private String organizationsFile;<a name="line.48"></a>
<FONT color="green">049</FONT>      private String collaborationsFile;<a name="line.49"></a>
<FONT color="green">050</FONT>      private String path;<a name="line.50"></a>
<FONT color="green">051</FONT>    <a name="line.51"></a>
<FONT color="green">052</FONT>      /**<a name="line.52"></a>
<FONT color="green">053</FONT>       * Initializes a new, empty model.<a name="line.53"></a>
<FONT color="green">054</FONT>       */<a name="line.54"></a>
<FONT color="green">055</FONT>      public IsernModel() {<a name="line.55"></a>
<FONT color="green">056</FONT>        this.ids = new HashSet&lt;Id&gt;();<a name="line.56"></a>
<FONT color="green">057</FONT>        this.researchers = new HashMap&lt;Id, Researcher&gt;();<a name="line.57"></a>
<FONT color="green">058</FONT>        this.organizations = new HashMap&lt;Id, Organization&gt;();<a name="line.58"></a>
<FONT color="green">059</FONT>        this.collaborations = new HashMap&lt;Id, Collaboration&gt;();<a name="line.59"></a>
<FONT color="green">060</FONT>      }<a name="line.60"></a>
<FONT color="green">061</FONT>    <a name="line.61"></a>
<FONT color="green">062</FONT>      /**<a name="line.62"></a>
<FONT color="green">063</FONT>       * Load data from files.<a name="line.63"></a>
<FONT color="green">064</FONT>       * <a name="line.64"></a>
<FONT color="green">065</FONT>       * @throws JAXBException if it cannot create a parser<a name="line.65"></a>
<FONT color="green">066</FONT>       * @throws IOException on bad input<a name="line.66"></a>
<FONT color="green">067</FONT>       */<a name="line.67"></a>
<FONT color="green">068</FONT>      public synchronized void load() throws JAXBException, IOException {<a name="line.68"></a>
<FONT color="green">069</FONT>        this.ids.clear();<a name="line.69"></a>
<FONT color="green">070</FONT>    <a name="line.70"></a>
<FONT color="green">071</FONT>        if (fileExists(this.researchersFile)) {<a name="line.71"></a>
<FONT color="green">072</FONT>          loadResearchers();<a name="line.72"></a>
<FONT color="green">073</FONT>        } else {<a name="line.73"></a>
<FONT color="green">074</FONT>          saveResearchers();<a name="line.74"></a>
<FONT color="green">075</FONT>        }<a name="line.75"></a>
<FONT color="green">076</FONT>        if (fileExists(this.organizationsFile) ) { <a name="line.76"></a>
<FONT color="green">077</FONT>          loadOrganizations();  <a name="line.77"></a>
<FONT color="green">078</FONT>        } else {<a name="line.78"></a>
<FONT color="green">079</FONT>          saveOrganizations();<a name="line.79"></a>
<FONT color="green">080</FONT>        }<a name="line.80"></a>
<FONT color="green">081</FONT>        if (fileExists(this.collaborationsFile) ) {<a name="line.81"></a>
<FONT color="green">082</FONT>          loadCollaborations();  <a name="line.82"></a>
<FONT color="green">083</FONT>        } else {<a name="line.83"></a>
<FONT color="green">084</FONT>          saveCollaborations();<a name="line.84"></a>
<FONT color="green">085</FONT>        }<a name="line.85"></a>
<FONT color="green">086</FONT>    <a name="line.86"></a>
<FONT color="green">087</FONT>        for (Organization organization : this.organizations.values()) {<a name="line.87"></a>
<FONT color="green">088</FONT>          this.fillAffiliatedResearchers(organization);<a name="line.88"></a>
<FONT color="green">089</FONT>        }<a name="line.89"></a>
<FONT color="green">090</FONT>        save();<a name="line.90"></a>
<FONT color="green">091</FONT>        //this.complete();<a name="line.91"></a>
<FONT color="green">092</FONT>      }<a name="line.92"></a>
<FONT color="green">093</FONT>    <a name="line.93"></a>
<FONT color="green">094</FONT>      /**<a name="line.94"></a>
<FONT color="green">095</FONT>       * Load Collaboration data from it's xml file.<a name="line.95"></a>
<FONT color="green">096</FONT>       * <a name="line.96"></a>
<FONT color="green">097</FONT>       * @throws JAXBException if it cannot create a parser<a name="line.97"></a>
<FONT color="green">098</FONT>       * @throws IOException on bad input<a name="line.98"></a>
<FONT color="green">099</FONT>       */<a name="line.99"></a>
<FONT color="green">100</FONT>      private void loadCollaborations() throws JAXBException, IOException {<a name="line.100"></a>
<FONT color="green">101</FONT>        this.collaborations.clear();<a name="line.101"></a>
<FONT color="green">102</FONT>        for (Collaboration c : ((Collaborations) JAXBContext.newInstance(Collaborations.class)<a name="line.102"></a>
<FONT color="green">103</FONT>            .createUnmarshaller().unmarshal(<a name="line.103"></a>
<FONT color="green">104</FONT>                new File(<a name="line.104"></a>
<FONT color="green">105</FONT>                    this.path + File.separatorChar + this.collaborationsFile))).getCollaboration()) {<a name="line.105"></a>
<FONT color="green">106</FONT>          addCollaboration(c);<a name="line.106"></a>
<FONT color="green">107</FONT>        }<a name="line.107"></a>
<FONT color="green">108</FONT>      }<a name="line.108"></a>
<FONT color="green">109</FONT>      <a name="line.109"></a>
<FONT color="green">110</FONT>      /**<a name="line.110"></a>
<FONT color="green">111</FONT>       * Load Organization data from it's xml  file.<a name="line.111"></a>
<FONT color="green">112</FONT>       * <a name="line.112"></a>
<FONT color="green">113</FONT>       * @throws JAXBException if it cannot create a parser<a name="line.113"></a>
<FONT color="green">114</FONT>       * @throws IOException on bad input<a name="line.114"></a>
<FONT color="green">115</FONT>       */<a name="line.115"></a>
<FONT color="green">116</FONT>      private void loadOrganizations() throws JAXBException, IOException {<a name="line.116"></a>
<FONT color="green">117</FONT>        this.organizations.clear();<a name="line.117"></a>
<FONT color="green">118</FONT>        for (Organization o : ((Organizations) JAXBContext.newInstance(Organizations.class)<a name="line.118"></a>
<FONT color="green">119</FONT>            .createUnmarshaller().unmarshal(<a name="line.119"></a>
<FONT color="green">120</FONT>                new File(<a name="line.120"></a>
<FONT color="green">121</FONT>                    this.path + File.separatorChar + this.organizationsFile))).getOrganization()) {<a name="line.121"></a>
<FONT color="green">122</FONT>          addOrganization(o);<a name="line.122"></a>
<FONT color="green">123</FONT>        }<a name="line.123"></a>
<FONT color="green">124</FONT>      }<a name="line.124"></a>
<FONT color="green">125</FONT>      <a name="line.125"></a>
<FONT color="green">126</FONT>      /**<a name="line.126"></a>
<FONT color="green">127</FONT>       * Load Researcher data from it's xml  file.<a name="line.127"></a>
<FONT color="green">128</FONT>       * <a name="line.128"></a>
<FONT color="green">129</FONT>       * @throws JAXBException if it cannot create a parser<a name="line.129"></a>
<FONT color="green">130</FONT>       * @throws IOException on bad input<a name="line.130"></a>
<FONT color="green">131</FONT>       */<a name="line.131"></a>
<FONT color="green">132</FONT>      private void loadResearchers() throws JAXBException, IOException {<a name="line.132"></a>
<FONT color="green">133</FONT>        this.researchers.clear();<a name="line.133"></a>
<FONT color="green">134</FONT>        for (Researcher r : ((Researchers) JAXBContext.newInstance(Researchers.class)<a name="line.134"></a>
<FONT color="green">135</FONT>            .createUnmarshaller().unmarshal(<a name="line.135"></a>
<FONT color="green">136</FONT>                new File(this.path + File.separatorChar + this.researchersFile))).getResearcher()) {<a name="line.136"></a>
<FONT color="green">137</FONT>          addResearcher(r);<a name="line.137"></a>
<FONT color="green">138</FONT>        }<a name="line.138"></a>
<FONT color="green">139</FONT>      }<a name="line.139"></a>
<FONT color="green">140</FONT>      <a name="line.140"></a>
<FONT color="green">141</FONT>      /**<a name="line.141"></a>
<FONT color="green">142</FONT>       * Complete all dangling references and sync both sides of double-sided relationships.<a name="line.142"></a>
<FONT color="green">143</FONT>       * <a name="line.143"></a>
<FONT color="green">144</FONT>       * Organization records trump researcher records, so that if the UH record says that Phil Johnson<a name="line.144"></a>
<FONT color="green">145</FONT>       * is affiliated, but the Phil Johnson record says his organization if UCXZ, Johnson ends up in<a name="line.145"></a>
<FONT color="green">146</FONT>       * UH.<a name="line.146"></a>
<FONT color="green">147</FONT>       */<a name="line.147"></a>
<FONT color="green">148</FONT>      private void complete() {<a name="line.148"></a>
<FONT color="green">149</FONT>    <a name="line.149"></a>
<FONT color="green">150</FONT>        // collab reference to organization<a name="line.150"></a>
<FONT color="green">151</FONT>        for (Collaboration c : this.collaborations.values()) {<a name="line.151"></a>
<FONT color="green">152</FONT>          if (c.getCollaboratingOrganizations() == null) {<a name="line.152"></a>
<FONT color="green">153</FONT>            continue;<a name="line.153"></a>
<FONT color="green">154</FONT>          }<a name="line.154"></a>
<FONT color="green">155</FONT>          for (String name : c.getCollaboratingOrganizations().getCollaboratingOrganization()) {<a name="line.155"></a>
<FONT color="green">156</FONT>    <a name="line.156"></a>
<FONT color="green">157</FONT>            // force org to exist<a name="line.157"></a>
<FONT color="green">158</FONT>            if (!this.organizations.containsKey(new Id(name))) {<a name="line.158"></a>
<FONT color="green">159</FONT>              Organization o = new Organization();<a name="line.159"></a>
<FONT color="green">160</FONT>              o.setName(name);<a name="line.160"></a>
<FONT color="green">161</FONT>              this.organizations.put(new Id(name), o);<a name="line.161"></a>
<FONT color="green">162</FONT>            }<a name="line.162"></a>
<FONT color="green">163</FONT>          }<a name="line.163"></a>
<FONT color="green">164</FONT>        }<a name="line.164"></a>
<FONT color="green">165</FONT>        <a name="line.165"></a>
<FONT color="green">166</FONT>        // org reference to researcher<a name="line.166"></a>
<FONT color="green">167</FONT>        for (Organization o : this.organizations.values()) {<a name="line.167"></a>
<FONT color="green">168</FONT>          if (o.getAffiliatedResearchers() == null) {<a name="line.168"></a>
<FONT color="green">169</FONT>            continue;<a name="line.169"></a>
<FONT color="green">170</FONT>          }<a name="line.170"></a>
<FONT color="green">171</FONT>          for (String name : o.getAffiliatedResearchers().getAffiliatedResearcher()) {<a name="line.171"></a>
<FONT color="green">172</FONT>            Researcher r;<a name="line.172"></a>
<FONT color="green">173</FONT>            Id resId = new Id(name);<a name="line.173"></a>
<FONT color="green">174</FONT>    <a name="line.174"></a>
<FONT color="green">175</FONT>            // force researcher to exist<a name="line.175"></a>
<FONT color="green">176</FONT>            if (this.researchers.containsKey(resId)) {<a name="line.176"></a>
<FONT color="green">177</FONT>              r = this.researchers.get(resId);<a name="line.177"></a>
<FONT color="green">178</FONT>            }<a name="line.178"></a>
<FONT color="green">179</FONT>            else {<a name="line.179"></a>
<FONT color="green">180</FONT>              r = new Researcher();<a name="line.180"></a>
<FONT color="green">181</FONT>              r.setName(name);<a name="line.181"></a>
<FONT color="green">182</FONT>              this.researchers.put(resId, r);<a name="line.182"></a>
<FONT color="green">183</FONT>            }<a name="line.183"></a>
<FONT color="green">184</FONT>    <a name="line.184"></a>
<FONT color="green">185</FONT>            // force researcher into org<a name="line.185"></a>
<FONT color="green">186</FONT>            r.setOrganization(o.getName());<a name="line.186"></a>
<FONT color="green">187</FONT>          }<a name="line.187"></a>
<FONT color="green">188</FONT>        }<a name="line.188"></a>
<FONT color="green">189</FONT>    <a name="line.189"></a>
<FONT color="green">190</FONT>        // researcher reference to organization<a name="line.190"></a>
<FONT color="green">191</FONT>        for (Researcher r : this.researchers.values()) {<a name="line.191"></a>
<FONT color="green">192</FONT>          String name = r.getOrganization();<a name="line.192"></a>
<FONT color="green">193</FONT>          Id orgId = new Id(name);<a name="line.193"></a>
<FONT color="green">194</FONT>          Organization o;<a name="line.194"></a>
<FONT color="green">195</FONT>          // force org to exist<a name="line.195"></a>
<FONT color="green">196</FONT>          if (this.organizations.containsKey(orgId)) {<a name="line.196"></a>
<FONT color="green">197</FONT>            o = this.organizations.get(orgId);<a name="line.197"></a>
<FONT color="green">198</FONT>          }<a name="line.198"></a>
<FONT color="green">199</FONT>          else {<a name="line.199"></a>
<FONT color="green">200</FONT>            o = new Organization();<a name="line.200"></a>
<FONT color="green">201</FONT>            o.setName(name);<a name="line.201"></a>
<FONT color="green">202</FONT>            o.setAffiliatedResearchers(new AffiliatedResearchers());<a name="line.202"></a>
<FONT color="green">203</FONT>            this.organizations.put(orgId, o);<a name="line.203"></a>
<FONT color="green">204</FONT>          }<a name="line.204"></a>
<FONT color="green">205</FONT>          // force researcher into org<a name="line.205"></a>
<FONT color="green">206</FONT>          if (!o.getAffiliatedResearchers().getAffiliatedResearcher().contains(r.getName())) {<a name="line.206"></a>
<FONT color="green">207</FONT>            o.getAffiliatedResearchers().getAffiliatedResearcher().add(r.getName());<a name="line.207"></a>
<FONT color="green">208</FONT>          }<a name="line.208"></a>
<FONT color="green">209</FONT>        }<a name="line.209"></a>
<FONT color="green">210</FONT>      }<a name="line.210"></a>
<FONT color="green">211</FONT>    <a name="line.211"></a>
<FONT color="green">212</FONT>      /**<a name="line.212"></a>
<FONT color="green">213</FONT>       * <a name="line.213"></a>
<FONT color="green">214</FONT>       * @param path the path to set<a name="line.214"></a>
<FONT color="green">215</FONT>       */<a name="line.215"></a>
<FONT color="green">216</FONT>      public synchronized void setPath(String path) {<a name="line.216"></a>
<FONT color="green">217</FONT>        this.path = path;<a name="line.217"></a>
<FONT color="green">218</FONT>      }<a name="line.218"></a>
<FONT color="green">219</FONT>    <a name="line.219"></a>
<FONT color="green">220</FONT>      /**<a name="line.220"></a>
<FONT color="green">221</FONT>       * Checks to see if a file exists in out application's data path. <a name="line.221"></a>
<FONT color="green">222</FONT>       * @param fileName Any filename.<a name="line.222"></a>
<FONT color="green">223</FONT>       * @return True if the file exists in our working directory.<a name="line.223"></a>
<FONT color="green">224</FONT>       */<a name="line.224"></a>
<FONT color="green">225</FONT>      private boolean fileExists(String fileName) {<a name="line.225"></a>
<FONT color="green">226</FONT>        return (new File(this.path + File.separatorChar + fileName)).exists() ;<a name="line.226"></a>
<FONT color="green">227</FONT>      }<a name="line.227"></a>
<FONT color="green">228</FONT>      <a name="line.228"></a>
<FONT color="green">229</FONT>      /**<a name="line.229"></a>
<FONT color="green">230</FONT>       * Return a Set of all IDs in use.<a name="line.230"></a>
<FONT color="green">231</FONT>       * <a name="line.231"></a>
<FONT color="green">232</FONT>       * @return a Set of IDs<a name="line.232"></a>
<FONT color="green">233</FONT>       */<a name="line.233"></a>
<FONT color="green">234</FONT>      public synchronized Set&lt;Id&gt; getIds() {<a name="line.234"></a>
<FONT color="green">235</FONT>        return this.ids;<a name="line.235"></a>
<FONT color="green">236</FONT>      }<a name="line.236"></a>
<FONT color="green">237</FONT>    <a name="line.237"></a>
<FONT color="green">238</FONT>      /**<a name="line.238"></a>
<FONT color="green">239</FONT>       * Return a map of current Researchers with IDs as keys.<a name="line.239"></a>
<FONT color="green">240</FONT>       * <a name="line.240"></a>
<FONT color="green">241</FONT>       * @return a map of Researchers<a name="line.241"></a>
<FONT color="green">242</FONT>       */<a name="line.242"></a>
<FONT color="green">243</FONT>      public synchronized Map&lt;Id, Researcher&gt; getResearchers() {<a name="line.243"></a>
<FONT color="green">244</FONT>        return this.researchers;<a name="line.244"></a>
<FONT color="green">245</FONT>      }<a name="line.245"></a>
<FONT color="green">246</FONT>    <a name="line.246"></a>
<FONT color="green">247</FONT>      /**<a name="line.247"></a>
<FONT color="green">248</FONT>       * Return a map of current Organizations with IDs as keys.<a name="line.248"></a>
<FONT color="green">249</FONT>       * <a name="line.249"></a>
<FONT color="green">250</FONT>       * @return a map of Organizations<a name="line.250"></a>
<FONT color="green">251</FONT>       */<a name="line.251"></a>
<FONT color="green">252</FONT>      public synchronized Map&lt;Id, Organization&gt; getOrganizations() {<a name="line.252"></a>
<FONT color="green">253</FONT>        return this.organizations;<a name="line.253"></a>
<FONT color="green">254</FONT>      }<a name="line.254"></a>
<FONT color="green">255</FONT>    <a name="line.255"></a>
<FONT color="green">256</FONT>      /**<a name="line.256"></a>
<FONT color="green">257</FONT>       * Return a map of current Collaborations with IDs as keys.<a name="line.257"></a>
<FONT color="green">258</FONT>       * <a name="line.258"></a>
<FONT color="green">259</FONT>       * @return a map of Collaborations<a name="line.259"></a>
<FONT color="green">260</FONT>       */<a name="line.260"></a>
<FONT color="green">261</FONT>      public Map&lt;Id, Collaboration&gt; getCollaborations() {<a name="line.261"></a>
<FONT color="green">262</FONT>        return this.collaborations;<a name="line.262"></a>
<FONT color="green">263</FONT>      }<a name="line.263"></a>
<FONT color="green">264</FONT>    <a name="line.264"></a>
<FONT color="green">265</FONT>      /**<a name="line.265"></a>
<FONT color="green">266</FONT>       * Check whether the Collaboration has an invalid year.<a name="line.266"></a>
<FONT color="green">267</FONT>       * <a name="line.267"></a>
<FONT color="green">268</FONT>       * @param c the Collaboration<a name="line.268"></a>
<FONT color="green">269</FONT>       * @return true if there is an invalid year<a name="line.269"></a>
<FONT color="green">270</FONT>       */<a name="line.270"></a>
<FONT color="green">271</FONT>      private static boolean hasBadYear(Collaboration c) {<a name="line.271"></a>
<FONT color="green">272</FONT>        boolean bad = false;<a name="line.272"></a>
<FONT color="green">273</FONT>        if (c.getYears() == null) {<a name="line.273"></a>
<FONT color="green">274</FONT>          return false;<a name="line.274"></a>
<FONT color="green">275</FONT>        }<a name="line.275"></a>
<FONT color="green">276</FONT>        for (BigInteger year : c.getYears().getYear()) {<a name="line.276"></a>
<FONT color="green">277</FONT>          if (year.longValue() &gt; 2010 || year.longValue() &lt; 1990) {<a name="line.277"></a>
<FONT color="green">278</FONT>            bad = true;<a name="line.278"></a>
<FONT color="green">279</FONT>          }<a name="line.279"></a>
<FONT color="green">280</FONT>        }<a name="line.280"></a>
<FONT color="green">281</FONT>        return bad;<a name="line.281"></a>
<FONT color="green">282</FONT>      }<a name="line.282"></a>
<FONT color="green">283</FONT>    <a name="line.283"></a>
<FONT color="green">284</FONT>      /**<a name="line.284"></a>
<FONT color="green">285</FONT>       * Save the data to files<a name="line.285"></a>
<FONT color="green">286</FONT>       * <a name="line.286"></a>
<FONT color="green">287</FONT>       * @throws IOException on save error<a name="line.287"></a>
<FONT color="green">288</FONT>       * @throws JAXBException if it cannot convert the objects to XML<a name="line.288"></a>
<FONT color="green">289</FONT>       */<a name="line.289"></a>
<FONT color="green">290</FONT>      public synchronized void save() throws IOException, JAXBException {<a name="line.290"></a>
<FONT color="green">291</FONT>    <a name="line.291"></a>
<FONT color="green">292</FONT>        // complete fixes references...<a name="line.292"></a>
<FONT color="green">293</FONT>        // this.complete();<a name="line.293"></a>
<FONT color="green">294</FONT>        saveResearchers();<a name="line.294"></a>
<FONT color="green">295</FONT>        saveOrganizations();<a name="line.295"></a>
<FONT color="green">296</FONT>        saveCollaborations();<a name="line.296"></a>
<FONT color="green">297</FONT>      }<a name="line.297"></a>
<FONT color="green">298</FONT>      /**<a name="line.298"></a>
<FONT color="green">299</FONT>       * Save the researcher data to files<a name="line.299"></a>
<FONT color="green">300</FONT>       * <a name="line.300"></a>
<FONT color="green">301</FONT>       * @throws IOException on save error<a name="line.301"></a>
<FONT color="green">302</FONT>       * @throws JAXBException if it cannot convert the objects to XML<a name="line.302"></a>
<FONT color="green">303</FONT>       */<a name="line.303"></a>
<FONT color="green">304</FONT>      public synchronized void saveResearchers() throws IOException, JAXBException {<a name="line.304"></a>
<FONT color="green">305</FONT>        Marshaller marshaller;<a name="line.305"></a>
<FONT color="green">306</FONT>        marshaller = JAXBContext.newInstance(Researchers.class).createMarshaller();<a name="line.306"></a>
<FONT color="green">307</FONT>        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);<a name="line.307"></a>
<FONT color="green">308</FONT>        Researchers researchers = new Researchers();<a name="line.308"></a>
<FONT color="green">309</FONT>        researchers.getResearcher().addAll(this.researchers.values());<a name="line.309"></a>
<FONT color="green">310</FONT>        marshaller.marshal(researchers, new FileOutputStream(this.path + File.separatorChar<a name="line.310"></a>
<FONT color="green">311</FONT>            + this.researchersFile));<a name="line.311"></a>
<FONT color="green">312</FONT>      }<a name="line.312"></a>
<FONT color="green">313</FONT>    <a name="line.313"></a>
<FONT color="green">314</FONT>      /**<a name="line.314"></a>
<FONT color="green">315</FONT>       * Save the organizations data to files<a name="line.315"></a>
<FONT color="green">316</FONT>       * <a name="line.316"></a>
<FONT color="green">317</FONT>       * @throws IOException on save error<a name="line.317"></a>
<FONT color="green">318</FONT>       * @throws JAXBException if it cannot convert the objects to XML<a name="line.318"></a>
<FONT color="green">319</FONT>       */<a name="line.319"></a>
<FONT color="green">320</FONT>      public synchronized void saveOrganizations() throws IOException, JAXBException {<a name="line.320"></a>
<FONT color="green">321</FONT>        Marshaller marshaller;<a name="line.321"></a>
<FONT color="green">322</FONT>        marshaller = JAXBContext.newInstance(Organizations.class).createMarshaller();<a name="line.322"></a>
<FONT color="green">323</FONT>        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);<a name="line.323"></a>
<FONT color="green">324</FONT>        Organizations organizations = new Organizations();<a name="line.324"></a>
<FONT color="green">325</FONT>        organizations.getOrganization().addAll(this.organizations.values());<a name="line.325"></a>
<FONT color="green">326</FONT>        marshaller.marshal(organizations, new FileOutputStream(this.path + File.separatorChar<a name="line.326"></a>
<FONT color="green">327</FONT>            + this.organizationsFile));<a name="line.327"></a>
<FONT color="green">328</FONT>      }<a name="line.328"></a>
<FONT color="green">329</FONT>    <a name="line.329"></a>
<FONT color="green">330</FONT>    <a name="line.330"></a>
<FONT color="green">331</FONT>      /**<a name="line.331"></a>
<FONT color="green">332</FONT>       * Save the Collaborations data to files.<a name="line.332"></a>
<FONT color="green">333</FONT>       * @throws JAXBException on save error<a name="line.333"></a>
<FONT color="green">334</FONT>       * @throws FileNotFoundException if it cannot convert the objects to XML<a name="line.334"></a>
<FONT color="green">335</FONT>       */<a name="line.335"></a>
<FONT color="green">336</FONT>      public synchronized void saveCollaborations() throws JAXBException, FileNotFoundException {<a name="line.336"></a>
<FONT color="green">337</FONT>        Marshaller marshaller;<a name="line.337"></a>
<FONT color="green">338</FONT>        marshaller = JAXBContext.newInstance(Collaborations.class).createMarshaller();<a name="line.338"></a>
<FONT color="green">339</FONT>        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);<a name="line.339"></a>
<FONT color="green">340</FONT>        Collaborations collaborations = new Collaborations();<a name="line.340"></a>
<FONT color="green">341</FONT>        collaborations.getCollaboration().addAll(this.collaborations.values());<a name="line.341"></a>
<FONT color="green">342</FONT>        marshaller.marshal(collaborations, new FileOutputStream(this.path + File.separatorChar<a name="line.342"></a>
<FONT color="green">343</FONT>            + this.collaborationsFile));<a name="line.343"></a>
<FONT color="green">344</FONT>      }<a name="line.344"></a>
<FONT color="green">345</FONT>    <a name="line.345"></a>
<FONT color="green">346</FONT>      /**<a name="line.346"></a>
<FONT color="green">347</FONT>       * Add a collaboration.<a name="line.347"></a>
<FONT color="green">348</FONT>       * <a name="line.348"></a>
<FONT color="green">349</FONT>       * @param collaboration the collaboration<a name="line.349"></a>
<FONT color="green">350</FONT>       * @throws IOException if there is already another entity with the same ID<a name="line.350"></a>
<FONT color="green">351</FONT>       */<a name="line.351"></a>
<FONT color="green">352</FONT>      public synchronized void addCollaboration(Collaboration collaboration) throws IOException {<a name="line.352"></a>
<FONT color="green">353</FONT>        Id id = new Id(collaboration.getName());<a name="line.353"></a>
<FONT color="green">354</FONT>        if (this.ids.contains(id) || this.collaborations.containsKey(id) || hasBadYear(collaboration)<a name="line.354"></a>
<FONT color="green">355</FONT>            || collaboration.getName().trim().equals("")) {<a name="line.355"></a>
<FONT color="green">356</FONT>          throw new IOException("Duplicate ID: " + id.toString());<a name="line.356"></a>
<FONT color="green">357</FONT>        }<a name="line.357"></a>
<FONT color="green">358</FONT>        else {<a name="line.358"></a>
<FONT color="green">359</FONT>          this.collaborations.put(id, collaboration);<a name="line.359"></a>
<FONT color="green">360</FONT>          this.ids.add(id);<a name="line.360"></a>
<FONT color="green">361</FONT>        }<a name="line.361"></a>
<FONT color="green">362</FONT>    <a name="line.362"></a>
<FONT color="green">363</FONT>      }<a name="line.363"></a>
<FONT color="green">364</FONT>    <a name="line.364"></a>
<FONT color="green">365</FONT>      /**<a name="line.365"></a>
<FONT color="green">366</FONT>       * Add an organization.<a name="line.366"></a>
<FONT color="green">367</FONT>       * <a name="line.367"></a>
<FONT color="green">368</FONT>       * @param organization the organization<a name="line.368"></a>
<FONT color="green">369</FONT>       * @throws IOException if there is already another entity with the same ID<a name="line.369"></a>
<FONT color="green">370</FONT>       */<a name="line.370"></a>
<FONT color="green">371</FONT>      public synchronized void addOrganization(Organization organization) throws IOException {<a name="line.371"></a>
<FONT color="green">372</FONT>        Id id = new Id(organization.getName());<a name="line.372"></a>
<FONT color="green">373</FONT>        if (this.ids.contains(id) || this.organizations.containsKey(id)<a name="line.373"></a>
<FONT color="green">374</FONT>            || organization.getName().trim().equals("")) {<a name="line.374"></a>
<FONT color="green">375</FONT>          throw new IOException("Duplicate ID: " + id);<a name="line.375"></a>
<FONT color="green">376</FONT>        }<a name="line.376"></a>
<FONT color="green">377</FONT>        else {<a name="line.377"></a>
<FONT color="green">378</FONT>          organizations.put(id, organization);<a name="line.378"></a>
<FONT color="green">379</FONT>          this.ids.add(id);<a name="line.379"></a>
<FONT color="green">380</FONT>        }<a name="line.380"></a>
<FONT color="green">381</FONT>      }<a name="line.381"></a>
<FONT color="green">382</FONT>    <a name="line.382"></a>
<FONT color="green">383</FONT>      /**<a name="line.383"></a>
<FONT color="green">384</FONT>       * Add researcher.<a name="line.384"></a>
<FONT color="green">385</FONT>       * <a name="line.385"></a>
<FONT color="green">386</FONT>       * @param researcher the researcher<a name="line.386"></a>
<FONT color="green">387</FONT>       * @throws IOException if there is already another entity with the same ID<a name="line.387"></a>
<FONT color="green">388</FONT>       */<a name="line.388"></a>
<FONT color="green">389</FONT>      public synchronized void addResearcher(Researcher researcher) throws IOException {<a name="line.389"></a>
<FONT color="green">390</FONT>        Id id = new Id(researcher.getName());<a name="line.390"></a>
<FONT color="green">391</FONT>        if (this.ids.contains(id) || <a name="line.391"></a>
<FONT color="green">392</FONT>            this.researchers.containsKey(id) || researcher.getName().trim().equals("")) {<a name="line.392"></a>
<FONT color="green">393</FONT>          throw new IOException("Duplicate ID: " + id);<a name="line.393"></a>
<FONT color="green">394</FONT>        }<a name="line.394"></a>
<FONT color="green">395</FONT>        else {<a name="line.395"></a>
<FONT color="green">396</FONT>          this.researchers.put(id, researcher);<a name="line.396"></a>
<FONT color="green">397</FONT>          this.udpateResearcherToOrganization(researcher);<a name="line.397"></a>
<FONT color="green">398</FONT>          this.ids.add(id);<a name="line.398"></a>
<FONT color="green">399</FONT>        }<a name="line.399"></a>
<FONT color="green">400</FONT>      }<a name="line.400"></a>
<FONT color="green">401</FONT>      <a name="line.401"></a>
<FONT color="green">402</FONT>      /**<a name="line.402"></a>
<FONT color="green">403</FONT>       * Update collaboration with the given id, overwriting the data with data in the <a name="line.403"></a>
<FONT color="green">404</FONT>       * provided object..<a name="line.404"></a>
<FONT color="green">405</FONT>       * <a name="line.405"></a>
<FONT color="green">406</FONT>       * @param id The Id for the given field.<a name="line.406"></a>
<FONT color="green">407</FONT>       * @param collaboration The collaboration object.<a name="line.407"></a>
<FONT color="green">408</FONT>       */<a name="line.408"></a>
<FONT color="green">409</FONT>      public synchronized void updateCollaboration(Id id, Collaboration collaboration) {<a name="line.409"></a>
<FONT color="green">410</FONT>        Id newId = new Id(collaboration.getName());<a name="line.410"></a>
<FONT color="green">411</FONT>        if (newId.toString().length() &lt; 1) {<a name="line.411"></a>
<FONT color="green">412</FONT>          return;<a name="line.412"></a>
<FONT color="green">413</FONT>        }         <a name="line.413"></a>
<FONT color="green">414</FONT>        if (!newId.equals(id)) {<a name="line.414"></a>
<FONT color="green">415</FONT>          this.getCollaborations().remove(id);<a name="line.415"></a>
<FONT color="green">416</FONT>          this.ids.remove(id);<a name="line.416"></a>
<FONT color="green">417</FONT>        }<a name="line.417"></a>
<FONT color="green">418</FONT>        this.getCollaborations().put(newId, collaboration);<a name="line.418"></a>
<FONT color="green">419</FONT>        this.ids.add(newId);<a name="line.419"></a>
<FONT color="green">420</FONT>      }<a name="line.420"></a>
<FONT color="green">421</FONT>    <a name="line.421"></a>
<FONT color="green">422</FONT>      /**<a name="line.422"></a>
<FONT color="green">423</FONT>       * Updates the researcher with the given id, overwriting the data with data in the <a name="line.423"></a>
<FONT color="green">424</FONT>       * provided object.<a name="line.424"></a>
<FONT color="green">425</FONT>       * <a name="line.425"></a>
<FONT color="green">426</FONT>       * @param id The Id for the given field.<a name="line.426"></a>
<FONT color="green">427</FONT>       * @param researcher The researcher object.<a name="line.427"></a>
<FONT color="green">428</FONT>       */<a name="line.428"></a>
<FONT color="green">429</FONT>      public synchronized void updateResearcher(Id id, Researcher researcher) {<a name="line.429"></a>
<FONT color="green">430</FONT>        Id newId = new Id(researcher.getName());<a name="line.430"></a>
<FONT color="green">431</FONT>        if (newId.toString().length() &lt; 1) {<a name="line.431"></a>
<FONT color="green">432</FONT>          return;<a name="line.432"></a>
<FONT color="green">433</FONT>        }        <a name="line.433"></a>
<FONT color="green">434</FONT>        try {<a name="line.434"></a>
<FONT color="green">435</FONT>          this.remove(id);<a name="line.435"></a>
<FONT color="green">436</FONT>        }<a name="line.436"></a>
<FONT color="green">437</FONT>        catch (IOException e) {<a name="line.437"></a>
<FONT color="green">438</FONT>          // TODO Auto-generated catch block<a name="line.438"></a>
<FONT color="green">439</FONT>          e.printStackTrace();<a name="line.439"></a>
<FONT color="green">440</FONT>        }<a name="line.440"></a>
<FONT color="green">441</FONT>        this.ids.add(newId);<a name="line.441"></a>
<FONT color="green">442</FONT>        this.researchers.put(newId, researcher);<a name="line.442"></a>
<FONT color="green">443</FONT>        //renew record<a name="line.443"></a>
<FONT color="green">444</FONT>        this.udpateResearcherToOrganization(researcher);<a name="line.444"></a>
<FONT color="green">445</FONT>      }<a name="line.445"></a>
<FONT color="green">446</FONT>    <a name="line.446"></a>
<FONT color="green">447</FONT>      /**<a name="line.447"></a>
<FONT color="green">448</FONT>       * Updates the organization with the given id, overwriting the data with data in the <a name="line.448"></a>
<FONT color="green">449</FONT>       * provided object.<a name="line.449"></a>
<FONT color="green">450</FONT>       * <a name="line.450"></a>
<FONT color="green">451</FONT>       * @param id The Id for the given field.<a name="line.451"></a>
<FONT color="green">452</FONT>       * @param organization The organization object with data to overwrite old organization.<a name="line.452"></a>
<FONT color="green">453</FONT>       */<a name="line.453"></a>
<FONT color="green">454</FONT>      public synchronized void updateOrganization(Id id, Organization organization) {<a name="line.454"></a>
<FONT color="green">455</FONT>        Id newId = new Id(organization.getName());<a name="line.455"></a>
<FONT color="green">456</FONT>        if (newId.toString().length() &lt; 1) {<a name="line.456"></a>
<FONT color="green">457</FONT>          return;<a name="line.457"></a>
<FONT color="green">458</FONT>        }        <a name="line.458"></a>
<FONT color="green">459</FONT>        if (!newId.equals(id)) {<a name="line.459"></a>
<FONT color="green">460</FONT>          this.getOrganizations().remove(id);<a name="line.460"></a>
<FONT color="green">461</FONT>          this.ids.remove(id);<a name="line.461"></a>
<FONT color="green">462</FONT>        }<a name="line.462"></a>
<FONT color="green">463</FONT>        this.getOrganizations().put(newId, organization);<a name="line.463"></a>
<FONT color="green">464</FONT>        this.ids.add(newId);<a name="line.464"></a>
<FONT color="green">465</FONT>        this.fillAffiliatedResearchers(organization);<a name="line.465"></a>
<FONT color="green">466</FONT>      }<a name="line.466"></a>
<FONT color="green">467</FONT>      <a name="line.467"></a>
<FONT color="green">468</FONT>      /**<a name="line.468"></a>
<FONT color="green">469</FONT>       * Retrieve a list of researchers affiliated to the organization's . <a name="line.469"></a>
<FONT color="green">470</FONT>       * <a name="line.470"></a>
<FONT color="green">471</FONT>       * @param organization the organization. <a name="line.471"></a>
<FONT color="green">472</FONT>       * @return a list of researcher names. <a name="line.472"></a>
<FONT color="green">473</FONT>       */<a name="line.473"></a>
<FONT color="green">474</FONT>      public synchronized List&lt;String&gt; retrieveAffiliatedResearchers(Organization organization) {<a name="line.474"></a>
<FONT color="green">475</FONT>        List&lt;String&gt; affiliatedResearchers = new ArrayList&lt;String&gt;();<a name="line.475"></a>
<FONT color="green">476</FONT>        if (organization != null) {<a name="line.476"></a>
<FONT color="green">477</FONT>          String orgName = organization.getName();<a name="line.477"></a>
<FONT color="green">478</FONT>          if (orgName != null) {<a name="line.478"></a>
<FONT color="green">479</FONT>            for (Researcher researcher : this.researchers.values()) {<a name="line.479"></a>
<FONT color="green">480</FONT>              if (orgName.equals(researcher.getOrganization()) ) {<a name="line.480"></a>
<FONT color="green">481</FONT>                affiliatedResearchers.add(researcher.getName());<a name="line.481"></a>
<FONT color="green">482</FONT>              }<a name="line.482"></a>
<FONT color="green">483</FONT>            }<a name="line.483"></a>
<FONT color="green">484</FONT>          }<a name="line.484"></a>
<FONT color="green">485</FONT>        }<a name="line.485"></a>
<FONT color="green">486</FONT>        return affiliatedResearchers;<a name="line.486"></a>
<FONT color="green">487</FONT>      }<a name="line.487"></a>
<FONT color="green">488</FONT>    <a name="line.488"></a>
<FONT color="green">489</FONT>      /**<a name="line.489"></a>
<FONT color="green">490</FONT>       * Fill the organization's affiliated researchers. <a name="line.490"></a>
<FONT color="green">491</FONT>       * <a name="line.491"></a>
<FONT color="green">492</FONT>       * @param organization the organization. <a name="line.492"></a>
<FONT color="green">493</FONT>       */<a name="line.493"></a>
<FONT color="green">494</FONT>      public synchronized void fillAffiliatedResearchers(Organization organization) {<a name="line.494"></a>
<FONT color="green">495</FONT>        if (organization != null) {<a name="line.495"></a>
<FONT color="green">496</FONT>          if (organization.getAffiliatedResearchers() == null) {<a name="line.496"></a>
<FONT color="green">497</FONT>            organization.setAffiliatedResearchers(new AffiliatedResearchers());<a name="line.497"></a>
<FONT color="green">498</FONT>          }<a name="line.498"></a>
<FONT color="green">499</FONT>          organization.getAffiliatedResearchers().getAffiliatedResearcher().clear();<a name="line.499"></a>
<FONT color="green">500</FONT>          organization.getAffiliatedResearchers().getAffiliatedResearcher().<a name="line.500"></a>
<FONT color="green">501</FONT>                                      addAll(this.retrieveAffiliatedResearchers(organization));<a name="line.501"></a>
<FONT color="green">502</FONT>          organization.getAffiliatedResearchers().getAffiliatedResearcher().<a name="line.502"></a>
<FONT color="green">503</FONT>                                      remove(organization.getContact());<a name="line.503"></a>
<FONT color="green">504</FONT>        }<a name="line.504"></a>
<FONT color="green">505</FONT>      }<a name="line.505"></a>
<FONT color="green">506</FONT>      <a name="line.506"></a>
<FONT color="green">507</FONT>      /**<a name="line.507"></a>
<FONT color="green">508</FONT>       * Add the researcher to his organization's affiliated researcher list.<a name="line.508"></a>
<FONT color="green">509</FONT>       * if his not the organization's contact. <a name="line.509"></a>
<FONT color="green">510</FONT>       * @param researcher the Researcher.<a name="line.510"></a>
<FONT color="green">511</FONT>       */<a name="line.511"></a>
<FONT color="green">512</FONT>      public synchronized void udpateResearcherToOrganization(Researcher researcher) {<a name="line.512"></a>
<FONT color="green">513</FONT>        if (researcher != null) {<a name="line.513"></a>
<FONT color="green">514</FONT>          Organization org = this.organizations.get(new Id(researcher.getOrganization()));<a name="line.514"></a>
<FONT color="green">515</FONT>          if (org != null &amp;&amp; researcher.getName() != null <a name="line.515"></a>
<FONT color="green">516</FONT>              &amp;&amp; !researcher.getName().equals(org.getContact())) {<a name="line.516"></a>
<FONT color="green">517</FONT>            if (org.getAffiliatedResearchers() == null) {<a name="line.517"></a>
<FONT color="green">518</FONT>              org.setAffiliatedResearchers(new AffiliatedResearchers());<a name="line.518"></a>
<FONT color="green">519</FONT>              org.getAffiliatedResearchers().getAffiliatedResearcher().add(researcher.getName());<a name="line.519"></a>
<FONT color="green">520</FONT>            }<a name="line.520"></a>
<FONT color="green">521</FONT>            else if (!org.getAffiliatedResearchers().getAffiliatedResearcher()<a name="line.521"></a>
<FONT color="green">522</FONT>                    .contains(researcher.getName())) {<a name="line.522"></a>
<FONT color="green">523</FONT>              org.getAffiliatedResearchers().getAffiliatedResearcher().add(researcher.getName());<a name="line.523"></a>
<FONT color="green">524</FONT>            }<a name="line.524"></a>
<FONT color="green">525</FONT>          }<a name="line.525"></a>
<FONT color="green">526</FONT>        }<a name="line.526"></a>
<FONT color="green">527</FONT>      }<a name="line.527"></a>
<FONT color="green">528</FONT>      <a name="line.528"></a>
<FONT color="green">529</FONT>      /**<a name="line.529"></a>
<FONT color="green">530</FONT>       * Remove a collaboration, organization or researcher, according to the id<a name="line.530"></a>
<FONT color="green">531</FONT>       * <a name="line.531"></a>
<FONT color="green">532</FONT>       * @param id the given Id.<a name="line.532"></a>
<FONT color="green">533</FONT>       * @throws IOException when matching object is not found.<a name="line.533"></a>
<FONT color="green">534</FONT>       */<a name="line.534"></a>
<FONT color="green">535</FONT>      public synchronized void remove(Id id) throws IOException {<a name="line.535"></a>
<FONT color="green">536</FONT>        if (this.ids.contains(id)) {<a name="line.536"></a>
<FONT color="green">537</FONT>          //=====remove collaboration======<a name="line.537"></a>
<FONT color="green">538</FONT>          if (this.collaborations.containsKey(id)) {<a name="line.538"></a>
<FONT color="green">539</FONT>            this.collaborations.remove(id);<a name="line.539"></a>
<FONT color="green">540</FONT>          }<a name="line.540"></a>
<FONT color="green">541</FONT>          //=====remove organization======<a name="line.541"></a>
<FONT color="green">542</FONT>          else if (this.organizations.containsKey(id)) {<a name="line.542"></a>
<FONT color="green">543</FONT>            String orgName = this.organizations.remove(id).getName();<a name="line.543"></a>
<FONT color="green">544</FONT>            for (Collaboration collaboration : this.collaborations.values()) {<a name="line.544"></a>
<FONT color="green">545</FONT>              collaboration.getCollaboratingOrganizations().getCollaboratingOrganization()<a name="line.545"></a>
<FONT color="green">546</FONT>                  .remove(orgName);<a name="line.546"></a>
<FONT color="green">547</FONT>            }<a name="line.547"></a>
<FONT color="green">548</FONT>          }<a name="line.548"></a>
<FONT color="green">549</FONT>          //=====remove researcher======<a name="line.549"></a>
<FONT color="green">550</FONT>          else if (this.researchers.containsKey(id)) {<a name="line.550"></a>
<FONT color="green">551</FONT>            Researcher researcher = this.researchers.remove(id);<a name="line.551"></a>
<FONT color="green">552</FONT>            Organization organization = this.organizations.get(new Id(researcher.getOrganization()));<a name="line.552"></a>
<FONT color="green">553</FONT>            if (organization != null &amp;&amp; organization.getContact() != null) {<a name="line.553"></a>
<FONT color="green">554</FONT>              if (organization.getContact().equals(researcher.getName())) {<a name="line.554"></a>
<FONT color="green">555</FONT>                organization.setContact("");<a name="line.555"></a>
<FONT color="green">556</FONT>              }<a name="line.556"></a>
<FONT color="green">557</FONT>              else if (organization.getAffiliatedResearchers() != null) {<a name="line.557"></a>
<FONT color="green">558</FONT>                organization.getAffiliatedResearchers().getAffiliatedResearcher()<a name="line.558"></a>
<FONT color="green">559</FONT>                    .remove(researcher.getName());<a name="line.559"></a>
<FONT color="green">560</FONT>              }<a name="line.560"></a>
<FONT color="green">561</FONT>            }<a name="line.561"></a>
<FONT color="green">562</FONT>          }<a name="line.562"></a>
<FONT color="green">563</FONT>          else {<a name="line.563"></a>
<FONT color="green">564</FONT>            this.ids.remove(id);<a name="line.564"></a>
<FONT color="green">565</FONT>            throw new IOException("ID in Set not matched any object: " + id);<a name="line.565"></a>
<FONT color="green">566</FONT>          }<a name="line.566"></a>
<FONT color="green">567</FONT>          this.ids.remove(id);<a name="line.567"></a>
<FONT color="green">568</FONT>        }<a name="line.568"></a>
<FONT color="green">569</FONT>        else {<a name="line.569"></a>
<FONT color="green">570</FONT>          throw new IOException("ID not found: " + id);<a name="line.570"></a>
<FONT color="green">571</FONT>        }<a name="line.571"></a>
<FONT color="green">572</FONT>      }<a name="line.572"></a>
<FONT color="green">573</FONT>      <a name="line.573"></a>
<FONT color="green">574</FONT>      /**<a name="line.574"></a>
<FONT color="green">575</FONT>       * Create new researcher.<a name="line.575"></a>
<FONT color="green">576</FONT>       * <a name="line.576"></a>
<FONT color="green">577</FONT>       * @param researcher The researcher object.<a name="line.577"></a>
<FONT color="green">578</FONT>       */<a name="line.578"></a>
<FONT color="green">579</FONT>      public synchronized void createResearcher(Researcher researcher) {<a name="line.579"></a>
<FONT color="green">580</FONT>        updateResearcher(null, researcher);<a name="line.580"></a>
<FONT color="green">581</FONT>      }<a name="line.581"></a>
<FONT color="green">582</FONT>    <a name="line.582"></a>
<FONT color="green">583</FONT>      /**<a name="line.583"></a>
<FONT color="green">584</FONT>       * Comparisons for organization collaboration levels<a name="line.584"></a>
<FONT color="green">585</FONT>       * <a name="line.585"></a>
<FONT color="green">586</FONT>       * @see #getOrganizationsByCollaborationLevel(CollabLevelCompare, int)<a name="line.586"></a>
<FONT color="green">587</FONT>       */<a name="line.587"></a>
<FONT color="green">588</FONT>      public enum CollabLevelCompare {<a name="line.588"></a>
<FONT color="green">589</FONT>        /** Same as given level */<a name="line.589"></a>
<FONT color="green">590</FONT>        EQUAL() {<a name="line.590"></a>
<FONT color="green">591</FONT>          /**<a name="line.591"></a>
<FONT color="green">592</FONT>           * Equality test<a name="line.592"></a>
<FONT color="green">593</FONT>           * <a name="line.593"></a>
<FONT color="green">594</FONT>           * @param a left-hand side<a name="line.594"></a>
<FONT color="green">595</FONT>           * @param b right-hand side<a name="line.595"></a>
<FONT color="green">596</FONT>           * @return true if equal<a name="line.596"></a>
<FONT color="green">597</FONT>           */<a name="line.597"></a>
<FONT color="green">598</FONT>          boolean isMatch(int a, int b) {<a name="line.598"></a>
<FONT color="green">599</FONT>            return a == b;<a name="line.599"></a>
<FONT color="green">600</FONT>          }<a name="line.600"></a>
<FONT color="green">601</FONT>        },<a name="line.601"></a>
<FONT color="green">602</FONT>    <a name="line.602"></a>
<FONT color="green">603</FONT>        /** Strictly greater than given level */<a name="line.603"></a>
<FONT color="green">604</FONT>        GREATER() {<a name="line.604"></a>
<FONT color="green">605</FONT>          /**<a name="line.605"></a>
<FONT color="green">606</FONT>           * Greater-than test<a name="line.606"></a>
<FONT color="green">607</FONT>           * <a name="line.607"></a>
<FONT color="green">608</FONT>           * @param a left-hand side<a name="line.608"></a>
<FONT color="green">609</FONT>           * @param b right-hand side<a name="line.609"></a>
<FONT color="green">610</FONT>           * @return true if strictly greater than<a name="line.610"></a>
<FONT color="green">611</FONT>           */<a name="line.611"></a>
<FONT color="green">612</FONT>          boolean isMatch(int a, int b) {<a name="line.612"></a>
<FONT color="green">613</FONT>            return a &gt; b;<a name="line.613"></a>
<FONT color="green">614</FONT>          }<a name="line.614"></a>
<FONT color="green">615</FONT>        };<a name="line.615"></a>
<FONT color="green">616</FONT>    <a name="line.616"></a>
<FONT color="green">617</FONT>        /**<a name="line.617"></a>
<FONT color="green">618</FONT>         * Check for a match between an organization's collaboration level and a target level.<a name="line.618"></a>
<FONT color="green">619</FONT>         * <a name="line.619"></a>
<FONT color="green">620</FONT>         * @param orgLevel the collaboration level of the organization<a name="line.620"></a>
<FONT color="green">621</FONT>         * @param targetLevel the target level<a name="line.621"></a>
<FONT color="green">622</FONT>         * @return true if there is a match<a name="line.622"></a>
<FONT color="green">623</FONT>         */<a name="line.623"></a>
<FONT color="green">624</FONT>        abstract boolean isMatch(int orgLevel, int targetLevel);<a name="line.624"></a>
<FONT color="green">625</FONT>      }<a name="line.625"></a>
<FONT color="green">626</FONT>    <a name="line.626"></a>
<FONT color="green">627</FONT>      /**<a name="line.627"></a>
<FONT color="green">628</FONT>       * Get organizations by collaborations level<a name="line.628"></a>
<FONT color="green">629</FONT>       * <a name="line.629"></a>
<FONT color="green">630</FONT>       * @param comp the type of comparison that determines whether an organization's collaboration<a name="line.630"></a>
<FONT color="green">631</FONT>       * level matches what we're looking for<a name="line.631"></a>
<FONT color="green">632</FONT>       * @param target the target level<a name="line.632"></a>
<FONT color="green">633</FONT>       * @return a map of matching organizations<a name="line.633"></a>
<FONT color="green">634</FONT>       */<a name="line.634"></a>
<FONT color="green">635</FONT>      public synchronized Map&lt;Id, Organization&gt; getOrganizationsByCollaborationLevel(<a name="line.635"></a>
<FONT color="green">636</FONT>                                                        CollabLevelCompare comp, int target) {<a name="line.636"></a>
<FONT color="green">637</FONT>        Map&lt;Id, Integer&gt; levels = new HashMap&lt;Id, Integer&gt;();<a name="line.637"></a>
<FONT color="green">638</FONT>    <a name="line.638"></a>
<FONT color="green">639</FONT>        // check the level of each org<a name="line.639"></a>
<FONT color="green">640</FONT>        for (Collaboration c : this.collaborations.values()) {<a name="line.640"></a>
<FONT color="green">641</FONT>          for (String name : c.getCollaboratingOrganizations().getCollaboratingOrganization()) {<a name="line.641"></a>
<FONT color="green">642</FONT>            Id id = new Id(name);<a name="line.642"></a>
<FONT color="green">643</FONT>            if (levels.containsKey(id)) {<a name="line.643"></a>
<FONT color="green">644</FONT>              levels.put(id, 1 + levels.get(id));<a name="line.644"></a>
<FONT color="green">645</FONT>            }<a name="line.645"></a>
<FONT color="green">646</FONT>            else {<a name="line.646"></a>
<FONT color="green">647</FONT>              levels.put(id, 1);<a name="line.647"></a>
<FONT color="green">648</FONT>            }<a name="line.648"></a>
<FONT color="green">649</FONT>          }<a name="line.649"></a>
<FONT color="green">650</FONT>        }<a name="line.650"></a>
<FONT color="green">651</FONT>    <a name="line.651"></a>
<FONT color="green">652</FONT>        // find matches<a name="line.652"></a>
<FONT color="green">653</FONT>        Map&lt;Id, Organization&gt; matches = new HashMap&lt;Id, Organization&gt;();<a name="line.653"></a>
<FONT color="green">654</FONT>        for (Id id : this.organizations.keySet()) {<a name="line.654"></a>
<FONT color="green">655</FONT>          if (comp.isMatch(levels.containsKey(id) ? levels.get(id) : 0, target)) {<a name="line.655"></a>
<FONT color="green">656</FONT>            matches.put(id, this.organizations.get(id));<a name="line.656"></a>
<FONT color="green">657</FONT>          }<a name="line.657"></a>
<FONT color="green">658</FONT>        }<a name="line.658"></a>
<FONT color="green">659</FONT>    <a name="line.659"></a>
<FONT color="green">660</FONT>        return matches;<a name="line.660"></a>
<FONT color="green">661</FONT>      }<a name="line.661"></a>
<FONT color="green">662</FONT>    <a name="line.662"></a>
<FONT color="green">663</FONT>      /**<a name="line.663"></a>
<FONT color="green">664</FONT>       * Get collaborations by organization<a name="line.664"></a>
<FONT color="green">665</FONT>       * <a name="line.665"></a>
<FONT color="green">666</FONT>       * @param orgId the organization to look for<a name="line.666"></a>
<FONT color="green">667</FONT>       * @return a map of collaborations involving the organization<a name="line.667"></a>
<FONT color="green">668</FONT>       */<a name="line.668"></a>
<FONT color="green">669</FONT>      public synchronized Map&lt;Id, Collaboration&gt; getCollaborationsByOrganization(Id orgId) {<a name="line.669"></a>
<FONT color="green">670</FONT>        return filterCollabs(CollabFilter.ORG_ID, orgId.toString());<a name="line.670"></a>
<FONT color="green">671</FONT>      }<a name="line.671"></a>
<FONT color="green">672</FONT>    <a name="line.672"></a>
<FONT color="green">673</FONT>      /**<a name="line.673"></a>
<FONT color="green">674</FONT>       * Get collaborations by year<a name="line.674"></a>
<FONT color="green">675</FONT>       * <a name="line.675"></a>
<FONT color="green">676</FONT>       * @param year the year to look for<a name="line.676"></a>
<FONT color="green">677</FONT>       * @return a map of collaborations that were happening in the given year<a name="line.677"></a>
<FONT color="green">678</FONT>       */<a name="line.678"></a>
<FONT color="green">679</FONT>      public synchronized Map&lt;Id, Collaboration&gt; getCollaborationsByYear(int year) {<a name="line.679"></a>
<FONT color="green">680</FONT>        return filterCollabs(CollabFilter.YEAR, Integer.toString(year));<a name="line.680"></a>
<FONT color="green">681</FONT>      }<a name="line.681"></a>
<FONT color="green">682</FONT>    <a name="line.682"></a>
<FONT color="green">683</FONT>      /**<a name="line.683"></a>
<FONT color="green">684</FONT>       * Get collaborations by researcher<a name="line.684"></a>
<FONT color="green">685</FONT>       * <a name="line.685"></a>
<FONT color="green">686</FONT>       * @param researcherId the ID of the researcher to look for<a name="line.686"></a>
<FONT color="green">687</FONT>       * @return a map of collaborations involving the organization to which the researcher belongs.<a name="line.687"></a>
<FONT color="green">688</FONT>       */<a name="line.688"></a>
<FONT color="green">689</FONT>      public synchronized Map&lt;Id, Collaboration&gt; getCollaborationsByResearcher(Id researcherId) {<a name="line.689"></a>
<FONT color="green">690</FONT>        if (this.researchers.containsKey(researcherId)) {<a name="line.690"></a>
<FONT color="green">691</FONT>          return getCollaborationsByOrganization(new Id(this.researchers.get(researcherId)<a name="line.691"></a>
<FONT color="green">692</FONT>              .getOrganization()));<a name="line.692"></a>
<FONT color="green">693</FONT>        }<a name="line.693"></a>
<FONT color="green">694</FONT>        else {<a name="line.694"></a>
<FONT color="green">695</FONT>          return emptyMap();<a name="line.695"></a>
<FONT color="green">696</FONT>        }<a name="line.696"></a>
<FONT color="green">697</FONT>      }<a name="line.697"></a>
<FONT color="green">698</FONT>    <a name="line.698"></a>
<FONT color="green">699</FONT>      /**<a name="line.699"></a>
<FONT color="green">700</FONT>       * Different ways of filtering the the Collaborations<a name="line.700"></a>
<FONT color="green">701</FONT>       * <a name="line.701"></a>
<FONT color="green">702</FONT>       * This is just an internal helper class.<a name="line.702"></a>
<FONT color="green">703</FONT>       */<a name="line.703"></a>
<FONT color="green">704</FONT>      private enum CollabFilter {<a name="line.704"></a>
<FONT color="green">705</FONT>        ORG_ID {<a name="line.705"></a>
<FONT color="green">706</FONT>          /**<a name="line.706"></a>
<FONT color="green">707</FONT>           * Check if a collaboration matches the target organization<a name="line.707"></a>
<FONT color="green">708</FONT>           * <a name="line.708"></a>
<FONT color="green">709</FONT>           * @param c the collaboration<a name="line.709"></a>
<FONT color="green">710</FONT>           * @param id the Id of target<a name="line.710"></a>
<FONT color="green">711</FONT>           * @return true if it matches<a name="line.711"></a>
<FONT color="green">712</FONT>           */<a name="line.712"></a>
<FONT color="green">713</FONT>          boolean isMatch(Collaboration c, String id) {<a name="line.713"></a>
<FONT color="green">714</FONT>            boolean match = false;<a name="line.714"></a>
<FONT color="green">715</FONT>            for (String name : c.getCollaboratingOrganizations().getCollaboratingOrganization()) {<a name="line.715"></a>
<FONT color="green">716</FONT>              if (new Id(name).equals(new Id(id))) {<a name="line.716"></a>
<FONT color="green">717</FONT>                match = true;<a name="line.717"></a>
<FONT color="green">718</FONT>              }<a name="line.718"></a>
<FONT color="green">719</FONT>            }<a name="line.719"></a>
<FONT color="green">720</FONT>            return match;<a name="line.720"></a>
<FONT color="green">721</FONT>          }<a name="line.721"></a>
<FONT color="green">722</FONT>        },<a name="line.722"></a>
<FONT color="green">723</FONT>    <a name="line.723"></a>
<FONT color="green">724</FONT>        YEAR {<a name="line.724"></a>
<FONT color="green">725</FONT>          /**<a name="line.725"></a>
<FONT color="green">726</FONT>           * Check if a collaboration matches the target year<a name="line.726"></a>
<FONT color="green">727</FONT>           * <a name="line.727"></a>
<FONT color="green">728</FONT>           * @param c the collaboration<a name="line.728"></a>
<FONT color="green">729</FONT>           * @param target the target<a name="line.729"></a>
<FONT color="green">730</FONT>           * @return true if it matches<a name="line.730"></a>
<FONT color="green">731</FONT>           */<a name="line.731"></a>
<FONT color="green">732</FONT>          boolean isMatch(Collaboration c, String target) {<a name="line.732"></a>
<FONT color="green">733</FONT>            boolean match = false;<a name="line.733"></a>
<FONT color="green">734</FONT>            for (BigInteger year : c.getYears().getYear()) {<a name="line.734"></a>
<FONT color="green">735</FONT>              if (year.equals(new BigInteger(target))) {<a name="line.735"></a>
<FONT color="green">736</FONT>                match = true;<a name="line.736"></a>
<FONT color="green">737</FONT>              }<a name="line.737"></a>
<FONT color="green">738</FONT>            }<a name="line.738"></a>
<FONT color="green">739</FONT>            return match;<a name="line.739"></a>
<FONT color="green">740</FONT>          }<a name="line.740"></a>
<FONT color="green">741</FONT>        };<a name="line.741"></a>
<FONT color="green">742</FONT>    <a name="line.742"></a>
<FONT color="green">743</FONT>        /**<a name="line.743"></a>
<FONT color="green">744</FONT>         * Check if a collaboration matches the target<a name="line.744"></a>
<FONT color="green">745</FONT>         * <a name="line.745"></a>
<FONT color="green">746</FONT>         * @param c the collaboration<a name="line.746"></a>
<FONT color="green">747</FONT>         * @param target the target<a name="line.747"></a>
<FONT color="green">748</FONT>         * @return true if it matches<a name="line.748"></a>
<FONT color="green">749</FONT>         */<a name="line.749"></a>
<FONT color="green">750</FONT>        abstract boolean isMatch(Collaboration c, String target);<a name="line.750"></a>
<FONT color="green">751</FONT>      }<a name="line.751"></a>
<FONT color="green">752</FONT>    <a name="line.752"></a>
<FONT color="green">753</FONT>      /**<a name="line.753"></a>
<FONT color="green">754</FONT>       * Applies the given filter to create a map of matching Collaborations.<a name="line.754"></a>
<FONT color="green">755</FONT>       * <a name="line.755"></a>
<FONT color="green">756</FONT>       * @param filter the filter<a name="line.756"></a>
<FONT color="green">757</FONT>       * @param target the filter parameter<a name="line.757"></a>
<FONT color="green">758</FONT>       * @return a map of all matching filters<a name="line.758"></a>
<FONT color="green">759</FONT>       */<a name="line.759"></a>
<FONT color="green">760</FONT>      private Map&lt;Id, Collaboration&gt; filterCollabs(CollabFilter filter, String target) {<a name="line.760"></a>
<FONT color="green">761</FONT>        Map&lt;Id, Collaboration&gt; matches = new HashMap&lt;Id, Collaboration&gt;();<a name="line.761"></a>
<FONT color="green">762</FONT>    <a name="line.762"></a>
<FONT color="green">763</FONT>        for (Map.Entry&lt;Id, Collaboration&gt; entry : this.collaborations.entrySet()) {<a name="line.763"></a>
<FONT color="green">764</FONT>          if (filter.isMatch(entry.getValue(), target)) {<a name="line.764"></a>
<FONT color="green">765</FONT>            matches.put(entry.getKey(), entry.getValue());<a name="line.765"></a>
<FONT color="green">766</FONT>          }<a name="line.766"></a>
<FONT color="green">767</FONT>        }<a name="line.767"></a>
<FONT color="green">768</FONT>        return matches;<a name="line.768"></a>
<FONT color="green">769</FONT>      }<a name="line.769"></a>
<FONT color="green">770</FONT>    <a name="line.770"></a>
<FONT color="green">771</FONT>      /**<a name="line.771"></a>
<FONT color="green">772</FONT>       * Gets a sorted list of the collaborations<a name="line.772"></a>
<FONT color="green">773</FONT>       * <a name="line.773"></a>
<FONT color="green">774</FONT>       * @return a list of collaborations, sorted by name<a name="line.774"></a>
<FONT color="green">775</FONT>       */<a name="line.775"></a>
<FONT color="green">776</FONT>      public synchronized List&lt;Collaboration&gt; getCollaborationList() {<a name="line.776"></a>
<FONT color="green">777</FONT>        return getDataList(this.collaborations);<a name="line.777"></a>
<FONT color="green">778</FONT>      }<a name="line.778"></a>
<FONT color="green">779</FONT>    <a name="line.779"></a>
<FONT color="green">780</FONT>      /**<a name="line.780"></a>
<FONT color="green">781</FONT>       * Gets a sorted list of the organizations<a name="line.781"></a>
<FONT color="green">782</FONT>       * <a name="line.782"></a>
<FONT color="green">783</FONT>       * @return a list of organizations, sorted by name<a name="line.783"></a>
<FONT color="green">784</FONT>       */<a name="line.784"></a>
<FONT color="green">785</FONT>      public synchronized List&lt;Organization&gt; getOrganizationList() {<a name="line.785"></a>
<FONT color="green">786</FONT>        return getDataList(this.organizations);<a name="line.786"></a>
<FONT color="green">787</FONT>      }<a name="line.787"></a>
<FONT color="green">788</FONT>    <a name="line.788"></a>
<FONT color="green">789</FONT>      /**<a name="line.789"></a>
<FONT color="green">790</FONT>       * Gets a sorted list of the researchers<a name="line.790"></a>
<FONT color="green">791</FONT>       * <a name="line.791"></a>
<FONT color="green">792</FONT>       * @return a list of researchers, sorted by name<a name="line.792"></a>
<FONT color="green">793</FONT>       */<a name="line.793"></a>
<FONT color="green">794</FONT>      public synchronized List&lt;Researcher&gt; getResearcherList() {<a name="line.794"></a>
<FONT color="green">795</FONT>        return getDataList(this.researchers);<a name="line.795"></a>
<FONT color="green">796</FONT>      }<a name="line.796"></a>
<FONT color="green">797</FONT>    <a name="line.797"></a>
<FONT color="green">798</FONT>      /**<a name="line.798"></a>
<FONT color="green">799</FONT>       * Returns a sorted list of the values in a Map with String keys.<a name="line.799"></a>
<FONT color="green">800</FONT>       * <a name="line.800"></a>
<FONT color="green">801</FONT>       * @param &lt;T&gt; the type of the data<a name="line.801"></a>
<FONT color="green">802</FONT>       * @param dataMap a map from strings to data<a name="line.802"></a>
<FONT color="green">803</FONT>       * @return a list of the data, sorted by the string keys<a name="line.803"></a>
<FONT color="green">804</FONT>       */<a name="line.804"></a>
<FONT color="green">805</FONT>      private &lt;T&gt; List&lt;T&gt; getDataList(Map&lt;Id, T&gt; dataMap) {<a name="line.805"></a>
<FONT color="green">806</FONT>        SortedSet&lt;Id&gt; ids = new TreeSet&lt;Id&gt;(dataMap.keySet());<a name="line.806"></a>
<FONT color="green">807</FONT>        List&lt;T&gt; dataList = new ArrayList&lt;T&gt;();<a name="line.807"></a>
<FONT color="green">808</FONT>        for (Id id : ids) {<a name="line.808"></a>
<FONT color="green">809</FONT>          dataList.add(dataMap.get(id));<a name="line.809"></a>
<FONT color="green">810</FONT>        }<a name="line.810"></a>
<FONT color="green">811</FONT>        return dataList;<a name="line.811"></a>
<FONT color="green">812</FONT>      }<a name="line.812"></a>
<FONT color="green">813</FONT>    <a name="line.813"></a>
<FONT color="green">814</FONT>      /**<a name="line.814"></a>
<FONT color="green">815</FONT>       * @param researchersFile the researchersFile to set<a name="line.815"></a>
<FONT color="green">816</FONT>       */<a name="line.816"></a>
<FONT color="green">817</FONT>      public synchronized void setResearchersFile(String researchersFile) {<a name="line.817"></a>
<FONT color="green">818</FONT>        this.researchersFile = researchersFile;<a name="line.818"></a>
<FONT color="green">819</FONT>      }<a name="line.819"></a>
<FONT color="green">820</FONT>    <a name="line.820"></a>
<FONT color="green">821</FONT>      /**<a name="line.821"></a>
<FONT color="green">822</FONT>       * @param organizationsFile the organizationsFile to set<a name="line.822"></a>
<FONT color="green">823</FONT>       */<a name="line.823"></a>
<FONT color="green">824</FONT>      public synchronized void setOrganizationsFile(String organizationsFile) {<a name="line.824"></a>
<FONT color="green">825</FONT>        this.organizationsFile = organizationsFile;<a name="line.825"></a>
<FONT color="green">826</FONT>      }<a name="line.826"></a>
<FONT color="green">827</FONT>    <a name="line.827"></a>
<FONT color="green">828</FONT>      /**<a name="line.828"></a>
<FONT color="green">829</FONT>       * <a name="line.829"></a>
<FONT color="green">830</FONT>       * @param collaborationsFile the collaborationsFile to set<a name="line.830"></a>
<FONT color="green">831</FONT>       */<a name="line.831"></a>
<FONT color="green">832</FONT>      public synchronized void setCollaborationsFile(String collaborationsFile) {<a name="line.832"></a>
<FONT color="green">833</FONT>        this.collaborationsFile = collaborationsFile;<a name="line.833"></a>
<FONT color="green">834</FONT>      }<a name="line.834"></a>
<FONT color="green">835</FONT>      <a name="line.835"></a>
<FONT color="green">836</FONT>    }<a name="line.836"></a>




























































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